Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats

Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.     

Genetic parameters for milk somatic cell score and relationship with production and udder type traits in dairy Alpine and Saanen primiparous goats

Goat milk somatic cell counts have been collected for several years in France by the national milk recording organization. Information is used for health management, because repeatedly elevated somatic cell counts are a good indirect predictor of intramammary infection. Genetic parameters were estimated for 67,882 and 49,709 primiparous goats of the dairy Alpine and Saanen breeds, respectively, with complete information for milk somatic cell counts and milk production traits. About 40% of the goats had additional information for 11 udder type traits scored by official classifiers of the breeders’ association CAPGENES. Estimates were obtained by REML with an animal model. The studied trait was lactation somatic cell score (LSCS), the weighted mean of somatic cell score (log-transformed SCC) adjusted for lactation stage. Heritability of LSCS was 0.20 and 0.24 in the Alpine and Saanen breeds, respectively. Relationships with milk production and udder type traits were additionally estimated by using multitrait analyses. Heritability estimates in first lactation ranged from 0.30 to 0.35 for lactation milk, fat, and protein yields; from 0.60 to 0.67 for fat and protein contents; and from 0.22 to 0.50 for udder type traits. Genetic correlations of somatic cell score with milk production traits were generally low, ranging from −0.13 to 0.12. Slightly more negative correlations were estimated for fat content: −0.18 and −0.20 in Saanen and Alpine breeds, respectively. Lactation somatic cell score was genetically correlated with udder floor position (r_g = −0.24 and −0.19 in the Alpine and Saanen breeds, respectively), and, in Saanen, teat length, teat width, and teat form (r_g = 0.29, 0.34 and −0.27, respectively). These results suggest that a reduction in somatic cell count can be achieved by selection while still improving milk production and udder type and teat traits.     

Accuracy of genomic evaluation with weighted single-step genomic best linear unbiased prediction for milk production traits,udder type traits,and somatic cell scores in French dairy goats

Genomic evaluation of French dairy goats is routinely conducted using the single-step genomic BLUP (ssGBLUP) method. This method has the advantage of simultaneously using all phenotypes, pedigrees, and genotypes. However, ssGBLUP assumes that all SNP explain the same amount of genetic variance, which is unlikely in the case of traits whose major genes or QTL are segregating. In this study, we investigated the effect of weighted ssGBLUP and its alternatives, which give more weight to SNP associated with the trait, on the accuracy of genomic evaluation of milk production, udder type traits, and somatic cell scores. The data set included 2,955 genotyped animals and 2,543,680 pedigree animals. The number of phenotypes varied with the trait. The accuracy of genomic evaluation was assessed on 205 genotyped Alpine and 146 genotyped Saanen goats born between 2009 and 2012. For traits with unknown QTL, weighted ssGBLUP was less accurate than, or as accurate as, ssGBLUP. For traits with identified QTL (i.e., QTL only present in the Saanen breed), weighted ssGBLUP outperformed ssGBLUP by between 2 and 14%.     

Single- and multiple-breed genomic evaluations for conformation traits in Canadian Alpine and Saanen dairy goats

Conformation traits are functional traits known to affect longevity, production efficiency, and profitability of dairy goats. However, genetic progress for these traits is expected to be slower than for milk production traits due to the limited number of herds participating in type classification programs, and often lower heritability estimates. Genomic selection substantially accelerates the rate of genetic progress in many species and industries, especially for lowly heritable, difficult, or expensive to measure traits. Therefore, the main objectives of this study were (1) to evaluate the potential benefits of the implementation of single-step genomic evaluations for conformation traits in Canadian Alpine and Saanen dairy goats, and (2) to investigate the effect of the use of single- and multiple-breed training populations. The phenotypes used in this study were linear conformation scores, on a 1-to-9 scale, for 8 traits (i.e., body capacity, dairy character, fore udder, feet and legs, general appearance, rear udder, medial suspensory ligament, and teats) of 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Averaged across all traits, the use of multiple-breed analyses increased validation accuracy for Saanen, and reduced bias of genomically enhanced breeding values (GEBV) for both Alpine and Saanen compared with single-breed analyses. Little benefit was observed from the use of GEBV relative to pedigree-based EBV in terms of validation accuracy and bias, possibly due to limitations in the validation design, but substantial gains of 0.14 to 0.21 (32–50%) were observed in the theoretical accuracy of validation animals when averaged across traits for single- and multiple-breed analyses. Across the whole genotyped population, average gains in theoretical accuracy for GEBV compared with EBV across all traits ranged from 0.15 to 0.17 (32–37%) for Alpine and 0.17 to 0.19 (40–41%) for Saanen, depending on the model used. The largest gains were observed for does without classification records (0.19–0.22 or 50–55%) and bucks without daughter classification records (0.20–0.27 or 57–82%), which have the least information contributing to their traditional EBV. The use of multiple-breed rather than single-breed models was most beneficial for the Saanen breed, which had fewer phenotypic records available for the analyses. These results suggest that the implementation of genomic selection could increase the accuracy of breeding values for conformation traits in Canadian dairy goats.     

Quantitative trait loci mapping of calving and conformation traits on Bos taurus autosome 18 in the German Holstein population

Linkage, linkage disequilibrium, and combined linkage and linkage disequilibrium analyses were performed to map quantitative trait loci (QTL) affecting calving and conformation traits on Bos taurus autosome 18 (BTA18) in the German Holstein population. Six paternal half-sib families consisting of a total of 1,054 animals were genotyped on 28 genetic markers in the telomeric region on BTA18 spanning approximately 30 Mb. Calving traits, body type traits, and udder type traits were investigated. Using univariately estimated breeding values, maternal and direct effects on calving ease and stillbirth were analyzed separately for first- and further-parity calvings. The QTL initially identified by separate linkage and linkage disequilibrium analyses could be confirmed by a combined linkage and linkage disequilibrium analysis for udder composite index, udder depth, fore udder attachment, front teat placement, body depth, rump angle, and direct effects on calving ease and stillbirth. Concurrence of QTL peaks and a similar shape of restricted log-likelihood ratio profiles were observed between udder type traits and for body depth and calving traits, respectively. Association analyses were performed for markers flanking the most likely QTL positions by applying a mixed model including a fixed allele effect of the maternally inherited allele and a random polygenic effect. Results indicated that microsatellite marker DIK4234 (located at 53.3 Mb) is associated with maternal effects on stillbirth, direct effects on calving ease, and body depth. A comparison of effects for maternally inherited DIK4234 alleles indicated a favorable, positive correlation of maternal and direct effects on calving. Additionally, the association of maternally inherited DIK4234 marker alleles with body depth implied that conformation traits might provide the functional background of the QTL for calving traits. For udder type traits, the strong coincidence of QTL peaks and the position of the QTL in a region previously reported to harbor QTL for somatic cell score indicated that effects of QTL for udder type traits might be correlated with effects of QTL for udder health traits on BTA18. Our results suggest that loci in the middle to telomeric region on BTA18 with effect on conformation traits may also contribute to the genetic variance of calving and udder health traits. Further analyses are required to identify the causal mutations affecting conformation and calving traits and to investigate the correlation of effects for loci associated with conformation, calving, and udder health traits.     

Using sequence variants of a QTL region improves the accuracy of genomic evaluation in French Saanen goats

The enhanced availability of sequence data in livestock provides an opportunity for more accurate predictions in routine genomic evaluations. Such evaluations would therefore no longer rely only on the linkage disequilibrium between a chip marker and the causal mutation. The objective of this study was to assess the usefulness of sequence data in Saanen goats (n = 33) to better capture a quantitative trait locus (QTL) on chromosome 19 (CHI19) and improve the accuracy of predictions for 3 milk production traits, 5 type traits, and somatic cell scores. All 1,207 50K genotypes were imputed to the sequence level. Four scenarios, each using a subset of CHI19 imputed variants, were then tested. Sequence-derived information included all CHI19 variants (529,576), all variants in the QTL region (22,269), 178 variants selected in the QTL region and added to an updated chip, or 178 randomly selected variants on CHI19. Two genomic evaluation models were applied: single-step genomic BLUP and weighted single-step genomic BLUP. All scenarios were compared with single-step genomic BLUP using 50K genotypes. Best overall results were obtained using single-step genomic BLUP on 50K genotypes completed with all variants in the QTL region of chromosome 19 (6.2% average increase in accuracy for 9 traits) with the highest accuracy gain for fat yield (17.9%), significant increases for milk (13.7%) and protein yields (12.5%), and type traits associated with CHI19. Despite its association with the QTL region of chromosome 19, the somatic cell score showed decreased accuracy in every alternative scenario. Using all CHI19 variants led to an overall decrease of 4.8% in prediction accuracy. The updated chip was efficient and improved genomic evaluations by 3.1 to 6.4% on average, depending on the scenario. Indeed, information from only a few carefully selected variants increased accuracies for traits of interest when used in a single-step genomic BLUP model. In conclusion, using QTL region variants imputed from sequence data in single-step genomic evaluations represents a promising perspective for such evaluations in dairy goats. Furthermore, using only a limited number of selected variants in QTL regions, as available on SNP chip updates, significantly increases the accuracy for QTL-associated traits without deteriorating the evaluation accuracy for other traits. The latter approach is interesting, as it avoids time-consuming imputation and data formatting processes and provides reliable genotypes.     

Characterization of Staphylococcus aureus isolated from chronically infected dairy goats

A herd of 88 Alpine goats in Northern Italy was monitored for a complete lactation. Milk samples were taken from each udder half during 8 monthly visits. Goats (n = 28) with ≥2 consecutive positive tests for Staphylococcus aureus in the same udder half were identified as chronically infected, and all of those had ≥4 positive tests of the 8 samples. Goats with no infections in either udder half during any visit were considered healthy (n = 26). Linear mixed models were used to examine the relationship between chronic infection by S. aureus and SCC and production traits. The bacteria isolated from one sample from each infected goat were genotyped on the basis of polymorphism in several genes and evaluated for the presence of genes encoding for enterotoxins. The bacteria isolated from each animal were also subject to a test for β-lactamase production and to minimum inhibitory concentration tests for 11 antimicrobial agents. As expected, SCC (log₂) was significantly higher in infected goats than in healthy goats (7.55 vs. 5.50). Also, mean log SCC from infected udder halves (8.02) was greater than that in uninfected udder halves from the same goats (6.44). No significant differences were observed in milk yield or for fat and protein percentages between infected and healthy goats. No genetic variability was observed among the bacteria isolated, suggesting that all were from the same strain, although isolates did vary in susceptibility to various antimicrobial agents. All S. aureus isolates were negative for the β-lactamase production test. The most effective drugs when tested in vitro were benzylpenicillin, amoxicillin plus clavulanic acid, cloxacillin, and cephalosporins.     

A first step toward genomic selection in the multi-breed French dairy goat population

The objectives of this study were to describe, using the goat SNP50 BeadChip (Illumina Inc., San Diego, CA), molecular data for the French dairy goat population and compare the effect of using genomic information on breeding value accuracy in different reference populations. Several multi-breed (Alpine and Saanen) reference population sizes, including or excluding female genotypes (from 67 males to 677 males, and 1,985 females), were used. Genomic evaluations were performed using genomic best linear unbiased predictor for milk production traits, somatic cell score, and some udder type traits. At a marker distance of 50 kb, the average r² (squared correlation coefficient) value of linkage disequilibrium was 0.14, and persistence of linkage disequilibrium as correlation of r-values among Saanen and Alpine breeds was 0.56. Genomic evaluation accuracies obtained from cross validation ranged from 36 to 53%. Biases of these estimations assessed by regression coefficients (from 0.73 to 0.98) of phenotypes on genomic breeding values were higher for traits such as protein yield than for udder type traits. Using the reference population that included all males and females, accuracies of genomic breeding values derived from prediction error variances (model accuracy) obtained for young buck candidates without phenotypes ranged from 52 to 56%. This was lower than the average pedigree-derived breeding value accuracies obtained at birth for these males from the official genetic evaluation (62%). Adding females to the reference population of 677 males improved accuracy by 5 to 9% depending on the trait considered. Gains in model accuracies of genomic breeding values ranged from 1 to 7%, lower than reported in other studies. The gains in breeding value accuracy obtained using genomic information were not as good as expected because of the limited size (at most 677 males and 1,985 females) and the structure of the reference population.     

Single-step genomic evaluation of milk production traits in Canadian Alpine and Saanen dairy goats

Genomic evaluations are routine in most plant and livestock breeding programs but are used infrequently in dairy goat breeding schemes. In this context, the purpose of this study was to investigate the use of the single-step genomic BLUP method for predicting genomic breeding values for milk production traits (milk, protein, and fat yields; protein and fat percentages) in Canadian Alpine and Saanen dairy goats. There were 6,409 and 12,236 Alpine records and 3,434 and 5,008 Saanen records for each trait in first and later lactations, respectively, and a total of 1,707 genotyped animals (833 Alpine and 874 Saanen). Two validation approaches were used, forward validation (i.e., animals born after 2013 with an average estimated breeding value accuracy from the full data set ≥0.50) and forward cross-validation (i.e., subsets of all animals included in the forward validation were used in successive replications). The forward cross-validation approach resulted in similar validation accuracies (0.55 to 0.66 versus 0.54 to 0.61) and biases (?0.01 to –0.07 versus ?0.03 to 0.11) to the forward validation when averaged across traits. Additionally, both single and multiple-breed analyses were compared, and similar average accuracies and biases were observed across traits. However, there was a small gain in accuracy from the use of multiple-breed models for the Saanen breed. A small gain in validation accuracy for genomically enhanced estimated breeding values (GEBV) relative to pedigree-based estimated breeding values (EBV) was observed across traits for the Alpine breed, but not for the Saanen breed, possibly due to limitations in the validation design, heritability of the traits evaluated, and size of the training populations. Trait-specific gains in theoretical accuracy of GEBV relative to EBV for the validation animals ranged from 17 to 31% in Alpine and 35 to 55% in Saanen, using the cross-validation approach. The GEBV predicted from the full data set were 12 to 16% more accurate than EBV for genotyped animals, but no gains were observed for nongenotyped animals. The largest gains were found for does without lactation records (35–41%) and bucks without daughter records (46–54%), and consequently, the implementation of genomic selection in the Canadian dairy goat population would be expected to increase selection accuracy for young breeding candidates. Overall, this study represents the first step toward implementation of genomic selection in Canadian dairy goat populations.     

Genome-wide association study of conformation and milk yield in mixed-breed dairy goats

Identification of genetic markers that affect economically important traits is of high value from a biological point of view, enabling the targeting of candidate genes and providing practical benefits for the industry such as wide-scale genomic selection. This study is one of the first to investigate the genetic background of economically important traits in dairy goats using the caprine 50K single nucleotide polymorphism (SNP) chip. The aim of the project was to perform a genome-wide association study for milk yield and conformation of udder, teat, and feet and legs. A total of 137,235 milk yield records on 4,563 goats each scored for 10 conformation traits were available. Out of these, 2,381 goats were genotyped with the Illumina Caprine 50K BeadChip (Illumina Inc., San Diego, CA). A range of pseudo-phenotypes were used including deregressed breeding values and pseudo-estimated breeding values. Genome-wide association studies were performed using the multi-locus mixed model (MLMM) algorithm implemented in SNP & Variation Suite v7.7.8 (Golden Helix Inc., Bozeman, MT). A genome-wise significant [−log₁₀(P-value) > 5.95] SNP for milk yield was identified on chromosome 19, with additional chromosome-wise significant (−log₁₀(P-value) > 4.46] SNP on chromosomes 4, 8, 14, and 29. Three genome-wise significant SNP for conformation of udder attachment, udder depth, and front legs were identified on chromosome 19, and chromosome-wise SNP were found on chromosomes 4, 5, 6, 10, 11, 12, 13, 14, 15, 16, 17, 18, 21, 23, and 27. The proportion of variance explained by the significant SNP was between 0.4 and 7.0% for milk yield and between 0.1 and 13.8% for conformation traits. This study is the first attempt to identify SNP associated with milk yield and conformation in dairy goats. Two genome-wise significant SNP for milk yield and 3 SNP for conformation of udder attachment, udder depth, and front legs were found. Our results suggest that conformation traits have a polygenic background because, for most of them, we did not identify any quantitative trait loci with major effect.     

Major quantitative trait loci influencing milk production and conformation traits in Guernsey dairy cattle detected on Bos taurus autosome 19

The goal of this study was to identify potential quantitative trait loci (QTL) for 27 production, fitness, and conformation traits of Guernsey cattle through genome-wide association (GWA) analyses, with extra emphasis on BTA19, where major QTL were observed for several traits. Animals' de-regressed predicted transmitting abilities (PTA) from the December 2018 traditional US evaluation were used as phenotypes. All of the Guernsey cattle included in the QTL analyses were predictor animals in the reference population, ranging from 1,077 to 1,685 animals for different traits. Single-trait GWA analyses were carried out by a mixed-model approach for all 27 traits using imputed high-density genotypes. A major QTL was detected on BTA19, influencing several milk production traits, conformation traits, and livability of Guernsey cattle, and the most significant SNP lie in the region of 26.2 to 28.3 Mb. The myosin heavy chain 10 (MYH10) gene residing within this region was found to be highly associated with milk production and body conformation traits of dairy cattle. After the initial GWA analyses, which suggested that many significant SNP are in linkage with one another, conditional analyses were used for fine mapping. The top significant SNP on BTA19 were fixed as covariables in the model, one at a time, until no more significant SNP were detected on BTA19. After this fine-mapping approach was applied, only 1 significant SNP was detected on BTA19 for most traits, but multiple, independent significant SNP were found for protein yield, dairy form, and stature. In addition, the haplotype that hosts the major QTL on BTA19 was traced to a US Guernsey born in 1954. The haplotype is common in the breed, indicating a long-term influence of this QTL on the US Guernsey population.     

Effect of subclinical intramammary infection on somatic cell counts and chemical composition of goats' milk

We investigated effects of subclinical intramammary infection (IMI) on milk somatic cell count (SCC) and milk composition in udder halves of dairy goats. A total of 35 mixed-age Alpine does (70 udder halves; approximately 55 kg body weight) were rotationally grazed on a mixture of vegetative forages (wheat/berseem clover, sudan grass and cowpeas). Milk samples for bacterial analysis and SCC were collected monthly from both halves from April to September, 2001. Across stages of lactation, 19-31% of udder halves became infected. The prevalence of IMI exhibited quadratic patterns through multi-peaked responses within each stage of lactation. Higher rates of IMI were observed during the early stage of lactation (19% in May) and in the late stage of lactation (31% in September). Coagulase negative Staphylococcus (CNS, 43.7%), Staph. aureus (35.4%), and Pseudomonas aeruginosa (12.4%) were the most prevalent pathogens. Within single-strain IMI, log SCC (6.24) was lower (P<0.01) for CNS than those derived from IMI by Staph. aureus (6.49), Ps. aeruginosa (6.53) or Serratia spp. (6.90). Infected udder halves had a higher average SCC (4761 v. 2259 x 10(3) cells/ml; P<0.01) than uninfected halves, but uninfected halves often had similar levels of SCC to infected halves. Daily average milk production was not significantly different between infected and non-infected goats and the relationship between IMI and SCC was not always correlated. Effective mastitis screening requires bacteriological culture since SCC was not highly correlated.     

Distribution of somatic cell count and udder pathogens in Norwegian dairy goats

Compared with dairy cows, goat somatic cell count (SCC) is higher and probably more affected by physiological factors such as parity, stage of lactation, and season. Thus, SCC is believed to be a less precise indicator of intramammary infections in dairy goats, and no consensus exists on SCC thresholds for considering goats as infected. The Norwegian Goat Recording System maintains individual goat production records and results from microbiological analyses of milk samples. In this retrospective observational study, we used recordings over a 10-yr period (2010 to 2020) to describe the association between individual goat SCC and noninfectious factors, as well as intramammary infections. The median SCC in the 1,000,802 milk recordings included in the study was 440,000 cells/mL, and the mode was 70,000 cells/mL. Somatic cell count increased with parity, days in milk, estrus, pasture season, and intramammary infections. The effect of parity and stage of lactation was significantly higher in infected compared with uninfected goats. Staphylococci dominated as causes of intramammary infections, with Staphylococcus aureus as the udder pathogen associated with highest SCC. The most prevalent non-aureus staphylococci were Staphylococcus warneri, Staphylococcus epidermidis, and Staphylococcus caprae. This study provides guidelines for interpretation of goat SCC at different parities and stages of lactations under Norwegian management conditions. We revealed a considerable variation in SCC associated with physiological factors, indicating that the cutoff for identifying infected goats should be a dynamic threshold adjusted for parity, stage of lactation, and season.     

A genome scan for quantitative trait loci affecting body conformation traits in Spanish Churra dairy sheep

A genome scan for chromosomal regions influencing body conformation traits was conducted for a population of Spanish Churra dairy sheep following a daughter design. A total of 739 ewes from 11 half-sib sire families were included in the study. The ewes were scored for the 5 linear traits used in the breeding scheme of the Churra breed to assess body conformation: stature, rear legs-rear view, foot angle, rump width, and general appearance. All the animals, including the 11 sires, were genotyped for 181 microsatellite markers evenly distributed across the 26 sheep autosomes. Using the yield deviations of the raw scores adjusted for fixed factors as phenotypic measurements, a quantitative trait loci (QTL) analysis was performed on the basis of a multi-marker regression method. Seven suggestive QTL were identified on chromosomes Ovis aries (OAR)2, OAR5, OAR16, OAR23, and OAR26, but none reached a genome-wise significance level. Putative QTL were identified for all of the traits analyzed, except for general appearance score. The suggestive QTL showing the highest test statistic influenced rear legs-rear view and was localized on OAR16, close to the growth hormone receptor coding gene, GHR. Some of the putative linkage associations reported here are consistent with previously reported QTL in cattle for similar traits. To the best of our knowledge, this study provides the first report of QTL for body conformation traits in dairy sheep; further studies will be needed to confirm and redefine the linkage associations reported herein. It is expected that future genome-wide association analyses of larger families will help identify genes underlying these putative genetic effects and provide useful markers for marker-assisted selection of such functional traits.     

Detection of quantitative trait loci and putative causal variants affecting somatic cell score in dairy sheep by using a 50K SNP chip and whole-genome sequencing

This study presents a scan of the ovine genome to identify quantitative trait loci (QTL) influencing the somatic cell score (SCS), a classical indicator of subclinical mastitis in sheep, and a subsequent high-resolution analysis of one of the identified QTL regions based on the analysis of whole-genome sequence data sets. A half-sib commercial population of Churra sheep genotyped with a 50K SNP chip was analyzed using linkage analysis (LA) and combined linkage and linkage disequilibrium analysis (LDLA). By LA, 2 5% chromosome-wide significant QTL on OAR5 and OAR25 and one 5% genome-wide significant QTL on ovine chromosome 20 (OAR20) were detected, whereas 22 significant associations were identified by LDLA. Two of the associations detected by LDLA replicated LA-detected effects (OAR20, OAR25). We compared the detected associations with previously reported QTL in sheep and cattle, and functional candidate genes were identified within the estimated confidence intervals. We then performed a high-resolution analysis of the OAR20 QTL region, the most significant QTL region identified by LA that replicated a QTL previously described in Churra sheep for SCS using microsatellite markers. For that, 2 segregating trios of 2 segregating families for the OAR20 QTL (each including the Qq sire and 2 daughters, QQ and qq) were selected for whole-genome sequencing. The bioinformatic analysis of the 6 sequenced samples performed across the genomic interval considered (14.2–41.7 Mb) identified a total of 227,030 variants commonly identified by 2 independent software packages. For the 3 different concordance tests considered, due to discrepancies regarding the QTL peak in the segregating families, the list of mutations concordant with the QTL segregating pattern was processed to identify the variants identified in immune-related genes that show a moderate/high impact on the encoded protein function. Among a list of 85 missense variants concordant with the QTL segregation pattern that were within candidate immune-related genes, 13 variants distributed across 7 genes [PKHD1, NOTCH4, AGER, ENSOARG00000009395 (HLA-C, Homo sapiens), ENSOARG00000015002 (HLA-B, H. sapiens), MOG, and ENSOARG00000018075 (BoLA, Bos taurus, orthologous to human HLA-A] were predicted to cause deleterious effects on protein function. Future studies should assess the possible associations of the candidate variants identified herein in commercial populations with indicator traits of udder inflammation (SCS, clinical mastitis).     

Genome-wide association study for age at puberty and resumption of cyclicity in a crossbred dairy cattle population

Fertility is of primary economic importance in dairy cattle and the most common reason for involuntary culling. However, standard fertility traits have very low heritability that renders genetic selection slow and difficult. In this study, we explored fertility from an endocrine standpoint. A total of 1,163 crossbred Holstein-Normande females in a 3-generation familial design were studied for progesterone level measured every 10 d to determine age at puberty (PUB) and commencement of postpartum luteal activity (CPLA). Genetic parameters were estimated using REML with WOMBAT software. The heritability estimates were 0.38 ± 0.10 and 0.16 ± 0.07 for PUB and CPLA, respectively. Moreover, the 2 traits were genetically correlated (0.45 ± 0.23), suggesting a partially common determinism. Because of the family structure, a linkage disequilibrium and linkage analysis approach was preferred over standard genome-wide association study to map genomic regions associated with these traits. Ten quantitative trait loci (QTL) were detected for PUB on chromosomes 1, 3, 11, 13, 14, 21, and 29, whereas 3 QTL were associated with CPLA on chromosomes 21 and 26. Only the QTL on chromosome 21 was common to both traits. Four functional candidate genes (NCOA2, GAS2, OVOL1, and FOSL1) were identified in the detected regions. These findings will contribute to a clearer understanding of fertility determinism and enhance the value of introducing endocrinological data in fertility studies.     

Quantitative trait loci underlying udder morphology traits in dairy sheep

A genome scan was conducted on the basis of the daughter design to detect quantitative trait loci (QTL) influencing udder morphology traits in Spanish Churra dairy sheep. A total of 739 ewes belonging to 11 half-sib families were genotyped for 182 microsatellite markers covering 3,248.2 cM (Kosambi) of the ovine autosomal genome. Phenotypic traits included scores for 5 linear udder traits: udder depth, udder attachment, teat placement, teat size, and udder shape. Quantitative measurements for the QTL analysis were calculated for each trait from evaluation scores using within-family yield deviations corrected for fixed environmental effects. Joint analysis of all families using Haley-Knott regression identified 5 regions that exceeded the 5% chromosome-wise significance threshold on chromosomes 7, 14, 15, 20, and 26. Based on the across-family results, a within-family analysis was carried out to identify families segregated according to the QTL and to estimate the QTL effect. The allelic substitution effect for individual families ranged from 0.47 to 1.7 phenotypic standard deviation units for udder shape on chromosome 15 and udder depth on chromosome 14, respectively. These QTL regions provide a starting point for further research aimed at the characterization of genetic variability involved in udder traits in Churra sheep. This paper presents the first report of a sheep genome scan for udder-related traits in a dairy sheep outbred population.     

Short communication: The unusual genetic trend of αS1-casein in Alpine and Saanen breeds

Genetic variation at the α_S1-casein locus (CSN1S1) is recognized as being crucial in the selection of dairy goats for cheese yield. At this locus, the existence of alleles that have strong, intermediate, weak, and null favorable effects on cheese yield and curd firmness is well known. Selection for alleles that have a strong favorable effect has been deliberately carried out, especially in France. In fact, the importance of α_S1-casein in selection was recently confirmed in the selling policies of semen, where bucks are marketed according to their genotypes. We evaluated genotypes and alleles frequencies at the α_S1-casein locus in 491 Italian Saanen and Alpine goats and compared them with previous data to investigate their evolution over the past decade. We also estimated soft cheese yield in a subset of the most represented genotypes to quantify the economic importance of considering the genetic trend of α_S1-casein genotype frequencies. We found a significant increase in frequency of the allele with the strongest favorable effect, A (+12 and +13%), and of the intermediate allele E (+17 and +7%) in Saanen and Alpine goats, respectively. Surprisingly, the frequency of the strong allele B decreased strikingly over time (−12% in Saanen, −6% in Alpine from 2004 to 2012). This is consistent with the current marketing of semen, in that bucks that are homozygous for strong (AA and BB) and intermediate alleles (EE) and even heterozygous for these alleles (BE and AE) are considered equal. It is worth noting that this practice strongly penalizes the best breeders that have flocks composed almost entirely of goats that are homozygous for strong alleles. For heterozygous goats, we estimated an economic loss of €85 and €215 per goat per lactation, respectively, for AE and BE, compare with AA and BB genotypes. The marketing of buck semen should clearly differentiate these 2 alleles to ensure the best economic genetic progress at this locus.     

Cheese yield,cheesemaking efficiency,and daily production of 6 breeds of goats

Little is known about the complex process of cheesemaking at the individual level of dairy goats because of the difficulties of producing a high number of model cheeses. The objectives of this work were (1) to study the cheesemaking ability of goat milk; (2) to investigate the variability of cheesemaking-related traits among different farms; (3) to assess the effects of stage of lactation and parity; and (4) to compare 6 breeds of goat (Saanen and Camosciata delle Alpi for the Alpine type; Murciano-Granadina, Maltese, Sarda and Sarda Primitiva for the Mediterranean type) for their cheesemaking ability. For each goat (n = 560) we studied (1) 8 milk quality traits (fat, protein, total solids, casein, lactose, pH, somatic cell score, and bacterial count); (2) 4 milk nutrient recovery traits (fat, protein, total solids, and energy) in curd; (3) 3 actual cheese yield traits (fresh cheese, cheese solids, and cheese water); (4) 2 theoretical cheese yield values (fresh cheese and cheese solids) and the related cheesemaking efficiencies; and (5) daily milk yield and 3 daily cheese yield traits (fresh cheese, cheese solids, and water retained in the curd). With respect to individual animal factors, farm was not particularly important for recovery traits or actual and theoretical cheese yield and estimates of efficiency, whereas it highly influenced daily productions. Parity of goats influenced daily cheese production, whereas DIM slightly affected recovery as well as percent and daily cheese yield traits. Breed was the most important source of variation for almost all cheesemaking traits. Compared with those of Alpine type, the 4 Mediterranean breeds had, on average, lower daily milk and cheese productions, greater actual and theoretical cheese yield, and higher recovery of nutrients in the curd. Among Alpine type, Camosciata delle Alpi was characterized by greater nutrients recovery than Saanen. Within the 4 Mediterranean types, the 3 Italians produced much less milk per day, with much more fat and protein and greater recovery traits than the Murciano-Granadina, resulting in greater actual cheese yield. Within the Italian breeds, milk from Sarda and Sarda Primitiva was characterized by lower daily yields, higher protein and fat content, and greater recoveries of nutrients than Maltese goats. These results confirmed the potential of goat milk for cheese production and could be useful to give new possibilities and direction in breeding programs.     

Correlations among linear type traits and somatic cell counts

Genetic and phenotypic correlations between linear type traits and SCC were estimated from lactation average SCC from Pennsylvania DHIA and Holstein linear type evaluations from Sire Power, Inc. and Holstein Association using REML. Correlations were estimated between linear type traits and SCC measured in first lactation and between linear type traits measured in first lactation and SCC measured in second or third lactation. Data sets ranged in size from 4294 daughters of 216 sires to 58,235 daughters of 301 sires. Phenotypic and genetic correlations between the linear traits that reflect body and locomotive characteristics and SCC were generally small and unimportant. Phenotypic correlations between udder traits and SCC were variable, but cows with higher udder depth scores (higher udders) had lower SCC. Genetic correlations between udder traits and SCC were also variable. Genetic correlations between SCC and udder depth, SCC and fore udder attachment, and SCC and teat placement were negative (favorable). Genetic correlations between teat length and SCC tended to be positive. Genetic correlations were largest in magnitude between udder depth and SCC and ranged from -.21 to -.64 (weighted mean = -.35). Selection for higher udders and closer teat placement will likely improve resistance to mastitis in dairy cattle.